The phrase was first used in songs by artists such as The Beatles and shortly after by Simon & Garfunkel. This phrase has absolutley no definitive meaning given by dictionaries or artists such as John Lennon who first used it. The phrase has two other widely known spellings: goo goo g'joob and kukukachu. It is believed to be used in songs and in 60s and 70s slang as a phrase left to be freely interpreted by anyone based on the surrounding context it is used in. The freedom to betsow any meaning upon the phrase makes the word a statement about freedom of expression, which is a meaning in itself.
Another widely accepted variation of the meaning is a slang way to assure the state of things is entirely fine; an expression of reassuring goodness. Also used as a way to introduce an effect or say "hey whatdya know--".
In "That '70s Show", Donna Pinciotti said coo coo ca choo as an end to a random string of rhymes while stoned.
Coo coo ca choo was also used by Crush the turtle in "Finding Nemo".

Man, you been a naughty boy, you let your face grow long.
I am the eggman, they are the eggmen.
I am the walrus, goo goo g'joob.
--The Beatles' "I Am The Walrus"

Hide it in a hiding place where no one ever goes
Put it in your pantry with your cupcakes
It's a little secret, just the Robinsons' affair
Most of all, you've got to hide it from the kids
Coo coo ca choo Mrs Robinson
--Simon & Garfunkel's "Mrs. Robinson"

Little dudes are just eggs, leave 'em
on the beach to hatch, then coo-coo-ca-choo, they find their way back to the big 'ol blue. --Crush from "Finding Nemo"